Thousands of years ago, hunter-gatherer societies existed near present-day Bogotá (at "El Abra" and "Tequendama") which traded with one another and with cultures living in the Magdalena River Valley. Beginning in the first millennium BC, groups of Amerindians developed the political system of "cacicazgos" with a pyramidal structure of power headed by caciques. Within Colombia, the two cultures with the most complex cacicazgo systems were the Tayronas in the Caribbean Region, and the Muiscas in the highlands around Bogotá, both of which were of the Chibcha language family. The Muisca people are considered to have had one of the most developed political systems in South America, after the Incas.

Spanish explorers made the first exploration of the Caribbean littoral in 1500 led by Rodrigo de Bastidas. Christopher Columbus navigated near the Caribbean in 1502. In 1508, Vasco Nuñez de Balboa started the conquest of the territory through the region of Urabá. In 1513, he was also the first European to discover the Pacific Ocean which he called Mar del Sur (or "Sea of the South") and which in fact would bring the Spaniards to Peru and Chile. In 1510, the first European city in the American Continent was founded, Santa María la Antigua del Darién in what is today the Chocó Department. The territory's main population was made up of hundreds of tribes of the Chibchan and Carib, currently known as the Caribbean people, whom the Spaniards conquered through warfare and alliances, while resulting disease and the conquest itself caused a demographic reduction among the indigenous. In the sixteenth century, Europeans began to bring slaves from Africa.

Since the beginning of the periods of Conquest and Colonization, there were several rebel movements under Spanish rule, most of them either being crushed or remaining too weak to change the overall situation. The last one, which sought outright independence from Spain, sprang up around 1810, following the independence of St. Domingue in 1804 (present day Haiti), who provided a non-negligible degree of support to the eventual leaders of this rebellion: Simón Bolívar and Francisco de Paula Santander. Simón Bolívar had become the first president of Colombia and Francisco de Paula Santander was Vice President; when Simón Bolívar stepped down, Santander became the second president of Colombia. The rebellion finally succeeded in 1819 when the territory of the Viceroyalty of New Granada became the Republic of Greater Colombia organized as a Confederation along Ecuador and Venezuela (Panama was part of Colombia).

Internal political and territorial divisions led to the secession of Venezuela and Quito (today's Ecuador) in 1830. At this time, the so-called "Department of Cundinamarca" adopted then the name "Nueva Granada", which it kept until 1856 when it became the "Confederación Granadina" (Grenadine Confederation). After a two year civil war in 1863, the "United States of Colombia" was created, lasting until 1886, when the country finally became known as the Republic of Colombia. Internal divisions remained between the bipartisan political forces, occasionally igniting very bloody civil wars, the most significant being the Thousand Days civil war (1899 - 1902) which together with the United States intentions to influence in the area (especially the Panama Canal construction and control) led to the separation of the Department of Panama in 1903 and the establishment of it as a nation. Colombia engulfed in a year long war with Peru over a territorial dispute involving the Amazonas Department and its capital Leticia. Soon after, Colombia achieved a relative degree of political stability, which was interrupted by a bloody conflict that took place between the late 1940s and the early 1950s, a period known as La Violencia ("The Violence"). Its cause was mainly because of mounting tensions between the two leading political parties, which subsequently ignited after the assassination of the Liberal Presidential candidate Jorge Eliécer Gaitán on April 9, 1948. This assassination caused riots in Bogotá and became known as El Bogotazo, the violence from these riots spread through out the country and claimed the lives of at least 180,000 Colombians. From 1953 to 1964 the violence between the two political parties decreased first when Gustavo Rojas deposed the President of Colombia in a coup d'etat, and negotiated with the guerrillas, and then under the military junta of General Gabriel París Gordillo.

After Rojas deposition the two political parties Colombian Conservative Party and Colombian Liberal Party agreed to the creation of a "National Front", whereby the Liberal and Conservative parties would govern jointly. The presidency would be determined by an alternating conservative and liberal president every 4 years for 16 years; the two parties would have parity in all other elective offices. The National Front ended "La Violencia", and National Front administrations attempted to institute far-reaching social and economic reforms in cooperation with the Alliance for Progress. In the end, the contradictions between each successive Liberal and Conservative administration made the results decidedly mixed. Despite the progress in certain sectors, many social and political injustices continued and many guerrillas were formally created such as the FARC, ELN and M-19 to fight the government and political apparatus with influences from Cold War doctrines.

Emerging in the late 1970s, powerful and violent drug cartels developed during the 1980s and 1990s. The Medellín Cartel under Pablo Escobar and the Cali Cartel, in particular, exerted political, economic and social influence in Colombia during this period. These cartels also financed and influenced different illegal armed groups throughout the political spectrum. Some enemies of these allied with the guerrillas and created or influenced paramilitary groups.

The new Colombian Constitution of 1991 was ratified after being drafted by the Constituent Assembly of Colombia. The constitution included key provisions on political, ethnic, human and gender rights. The new constitution initially prohibited the extradition of Colombian nationals. There were accusations of lobbying by drug cartels in favor of this prohibition. The cartels had previously promoted a violent campaign against extradition, leading to many terrorist attack and mafia style executions. They also tried to influence the government and political structure of Colombia by means of corruption, as in the case of the 8000 Process scandal.

In recent years, the country has continued to be plagued by the effects of the drug trade, guerrilla insurgencies like FARC and paramilitary groups such as the AUC (later demobilized, though paramilitarism remains active), which along with other minor factions have engaged in a bloody internal armed conflict. President Andrés Pastrana and the FARC attempted to negotiate a solution to the conflict between 1998 and 2002 but failed to do so. President Andrés Pastrana also began to implement the Plan Colombia initiative, with the dual goal of ending the armed conflict and promoting a strong anti-narcotic strategy.

During the presidency of Álvaro Uribe, who was elected on the promise of applying military pressure on the FARC and other criminal groups, some security indicators have improved, showing a decrease in reported kidnappings (from 3700 in the year 2000 to 800 in 2005) and a decrease of more than 48% in homicides between July 2002 and May 2005 and of the terrorist guerrila itself reduced from 16.900 insurgents to 8.900 insurgents. It is argued that these improvements have favored economic growth and tourism. The 2006–2007 Colombian parapolitics scandal emerged due to the revelations and judicial implications of past and present links between paramilitary groups, mainly the AUC, and some government officials and many politicians, most of them allied to the governing administration.

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